I am trying to use BWA-MEM in Galaxy to align fastq files to mouse genome. I am having an issue with selecting the fastq dataset option. All fastq files have been uploaded to my history. How do I get the workflow to recognize these files?

Hi Jen, thanks for pointing me in the right direction. When I go to the Fastq Groomer function, I need to select the correct quality scores type, but there are only 4 listed and none of them is for Nanopore sequencing. Any idea what I should select? Just trying each one failed to have the command executed.